System.err.println(dir.listFiles()[k].getAbsolutePath());
MDLV2000Reader reader = new MDLV2000Reader(new FileInputStream(dir.listFiles()[k]), Mode.RELAXED);
IAtomContainer cdkmol = (IAtomContainer)reader.read(DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class));
String inputstr = getMolSvg(cdkmol, 100, 100);
ImageTranscoder imageTranscoder = new JPEGTranscoder();
imageTranscoder.addTranscodingHint(JPEGTranscoder.KEY_QUALITY, new Float(.8));
TranscoderInput input = new TranscoderInput(new StringReader(inputstr));
FileOutputStream ostream = new FileOutputStream(new File(dir.listFiles()[k].getAbsolutePath().substring(0,dir.listFiles()[k].getAbsolutePath().length()-4)+".png"));
TranscoderOutput output = new TranscoderOutput(ostream);
imageTranscoder.transcode(input, output);
ostream.flush();